Variant report

Variant	rs2290546
Chromosome Location	chr3:46965197-46965198
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46963604..46965379-chr3:47041668..47043184,2	K562	blood:
2	chr3:46964872..46965611-chr3:47030738..47031577,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYL3-1	chr3:46963238-46965649	NONHSAT089464

Variant related genes	Relation type
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001284	0.93[ASN][1000 genomes]
rs10461018	0.87[JPT][hapmap]
rs1079276	0.82[JPT][hapmap]
rs10865943	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130110	0.87[JPT][hapmap]
rs11130111	0.82[JPT][hapmap]
rs1138518	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11705936	0.97[ASN][1000 genomes]
rs11719795	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13061071	0.81[JPT][hapmap]
rs1466275	0.91[ASN][1000 genomes]
rs2061197	0.87[JPT][hapmap]
rs2168443	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs2242116	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2290545	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2305634	0.81[JPT][hapmap]
rs2305638	0.82[JPT][hapmap]
rs4078466	0.81[JPT][hapmap]
rs4082155	0.81[JPT][hapmap]
rs4539969	0.91[ASN][1000 genomes]
rs4587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682837	0.83[JPT][hapmap]
rs4682844	0.87[JPT][hapmap]
rs4682845	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683294	0.91[CEU][hapmap]
rs4683296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683298	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683299	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683300	0.92[ASN][1000 genomes]
rs4683301	0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs6442038	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442039	0.91[ASN][1000 genomes]
rs6442040	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6780601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724448	0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs724449	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs724450	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7623898	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628747	0.87[JPT][hapmap]
rs7635480	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7646906	0.94[ASN][1000 genomes]
rs9852082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9855938	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290546	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46956400-46965200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr3:46956600-46967200	Strong transcription	Thymus	Thymus
3	chr3:46956800-46966600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:46957000-46965400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr3:46957800-46966600	Strong transcription	Fetal Thymus	thymus
6	chr3:46957800-46967200	Strong transcription	HSMM	muscle
7	chr3:46958200-46966800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr3:46958200-46967200	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr3:46958200-46967600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:46958200-46968200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr3:46958200-46968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:46958400-46965200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:46958400-46965200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:46958400-46966800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:46958400-46967200	Strong transcription	HMEC	breast
16	chr3:46958400-46967600	Strong transcription	Primary T cells from cord blood	blood
17	chr3:46958400-46967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:46958400-46968200	Strong transcription	Dnd41	blood
19	chr3:46958600-46965200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:46958600-46965200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:46958600-46965200	Strong transcription	Fetal Intestine Large	intestine
22	chr3:46958600-46965600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr3:46958600-46966400	Strong transcription	Placenta	Placenta
24	chr3:46958600-46966600	Strong transcription	Adipose Nuclei	Adipose
25	chr3:46958600-46966800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:46958600-46966800	Strong transcription	HSMMtube	muscle
27	chr3:46958600-46967000	Strong transcription	Brain Anterior Caudate	brain
28	chr3:46958600-46967200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:46958600-46967400	Strong transcription	Liver	Liver
30	chr3:46958600-46967800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:46958600-46968000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:46958600-46970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:46958800-46965400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:46958800-46967200	Strong transcription	NH-A	brain
35	chr3:46958800-46967600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:46958800-46967600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:46958800-46967800	Strong transcription	Osteobl	bone
38	chr3:46959000-46965200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:46959000-46971400	Strong transcription	K562	blood
40	chr3:46959400-46966600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:46959400-46967200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:46959400-46967200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:46959400-46967200	Strong transcription	Brain Angular Gyrus	brain
44	chr3:46959400-46967600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:46959400-46968200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:46959600-46965200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:46959600-46967000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:46959600-46967400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:46959600-46970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:46959800-46968000	Strong transcription	Fetal Stomach	stomach

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